The NCBI Datasets Project

https://www.ncbi.nlm.nih.gov/datasets

National Center for Biotechnology Information, U.S. National Library of Medicine

The NCBI Datasets Project has developed virus-specific genome and protein datasets, initially limited to the Coronaviridae (NCBI Taxonomy ID: 11118) family of viruses, in response to the COVID-19 pandemic.

Viral genome data is currently limited to all Coronaviridae (Taxonomy ID: 11118) including SARS-CoV-2 (SARS2, Taxonomy ID: 2697049).

Viral protein data is currently limited to SARS-CoV-2 (SARS2) only.

To request SARS-CoV-2 protein data, you must use one of the following one-word terms, with one allowed term per protein: orf1ab (orf1ab polyprotein), orf1a (orf1a polyprotein), nsp1 (leader protein), nsp2, nsp3, nsp4, nsp5 (3C-like proteinase), nsp6, nsp7, nsp8, nsp9, nsp10, RdRp (RNA-dependent RNA polymerase or nsp12), nsp11, nsp13 (helicase), nsp14 (3'-to-5' exonuclease), nsp15 (endoRNAse), nsp16 (2'-O-ribose methyltransferase), S (surface glycoprotein or spike protein), ORF3a, E (envelope protein or ORF4), M (membrane glycoprotein or ORF5), ORF6, ORF7a, ORF7b, ORF8, N (nucleocapsid phosphoprotein or ORF9), ORF10.

The table below describes the contents of each of the files that may be included in your download.

File Name                   Description
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CDS.fna                     FASTA nucleotide sequence file containing RefSeq and GenBank coding sequences of polyproteins, mature peptides processed from polyproteins and other proteins.

protein.faa                 FASTA amino acid sequence file containing RefSeq and GenBank protein sequences, including polyproteins, mature peptides processed from polyproteins and other proteins.

genomic.fna                 FASTA nucleotide sequence file containing RefSeq and GenBank genome sequences.

genomic.gbff                GenBank flat file containing genome sequences and annotation.

protein.gpff                GenPept flat file containing protein sequences and annotation.

/pdb/*.pdb                  Protein databank files describing the three-dimensional structure, with annotation and metadata, for a subset of SARS-CoV-2 proteins.

data_report.jsonl           Virus-specific data report contains accession, taxonomy, isolate, host, release date and other metadata.

dataset_catalog.json        List of files and file types.
